19-4664907-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019107.4(MYDGF):c.256G>A(p.Asp86Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000446 in 1,613,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019107.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYDGF | ENST00000262947.8 | c.256G>A | p.Asp86Asn | missense_variant | Exon 3 of 6 | 1 | NM_019107.4 | ENSP00000262947.2 | ||
MYDGF | ENST00000599630.1 | c.256G>A | p.Asp86Asn | missense_variant | Exon 3 of 5 | 2 | ENSP00000469945.1 | |||
MYDGF | ENST00000596031.1 | n.133G>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 3 | |||||
MYDGF | ENST00000599761.5 | c.-3G>A | upstream_gene_variant | 3 | ENSP00000469136.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000233 AC: 58AN: 249254Hom.: 0 AF XY: 0.000192 AC XY: 26AN XY: 135250
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1460680Hom.: 0 Cov.: 30 AF XY: 0.0000385 AC XY: 28AN XY: 726628
GnomAD4 genome AF: 0.0000459 AC: 7AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.256G>A (p.D86N) alteration is located in exon 3 (coding exon 3) of the MYDGF gene. This alteration results from a G to A substitution at nucleotide position 256, causing the aspartic acid (D) at amino acid position 86 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at